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CS190/295 Programming in Python for
Life Sciences: Lecture 1
Instructor: Xiaohui Xie
University of California, Irvine
Today’s Goals
• Course information
• A basic introduction to computers and programs
Course Information
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Lecture: TT 3:30-4:50pm in ELH 110
Office hours: TT after class
Course Prerequisites: none
TA: Jake Biesinger
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Email: [email protected]
Office: BH 4082
Grading based on
– Homework (5-8 assignments); no exams
Course Goals
• Introduction to computer programming using
python
• Primary targets of audience:
– Students in bio or med areas who are interested in
learning a programming language
– Or students in other areas who are interested in using
computers to solve life science problems
References
• Recommended textbook:
 Python Programming: An Introduction to Computer
Science, 2nd, John Zelle
• Lecture notes, references and assignments will be available
from the course website (website link available from EEE)
Teaching format of the course
We will alternate between regular lectures and lab
sessions.
• Regular lectures (basic programming techniques,
concepts)
• Lab sessions, led by Jake Biesinger. Attendance is
required. This is the way you will practice and
improve your programming skills!
Topics to be covered
• Basic programming concepts:
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Intro to computers and programs
Write simple programs
Computing with numbers
Sequences: strings, lists and files
Functions
Loop structures
Classes and object-oriented design
• Applications in life sciences
– Examples from biological and medical areas
Chapter 1: Computers and Programs
Hardware Basics
 CPU (central processing unit) - the “brain” of the machine, where all the
basic operations are carried out, such as adding two numbers or do logical
operations
 Main Memory – stores programs & data. CPU can ONLY directly access info
stored in the main memory, called RAM (Random Access Memory). Main
memory is fast, but volatile.
 Secondary Memory – provides more permanent storage
o Hard disk (magnetic)
o Optical discs
o Flash drives
 Input Devices – keyboard, mouse, etc
 Output Device – monitor, printer, etc
How does CPU execute a program?
The instructions that comprise the program are
copied from the secondary memory to the main
memory
CPU start executing the program, following a
process called the fetch execute cycle
1. Retrieve the first instruction from memory
2. Decode its presentation
3. Perform the appropriate action
Fetch, decode,
and execute the
next instruction
Programming Languages
 A program is simply a sequence of instructions
telling a computer what to do.
 Programming languages are special notations for
expressing computations in an exact, and
unambiguous way
 Every structure in a program language has a precise
form (its syntax) and a precise meaning (its semantics)
 Python is one example of a programming
language. Others include C++, Fortran, Java, Perl,
Matlab, …
High-level vs. machine language
 Python, C++, Fortran, Java, and Perl are highlevel computer languages, designed to be used
and understood by humans.
 However, CPU can only understand very low-level
language known as machine language
High-level vs. machine language
Suppose we want the computer to add two numbers.
The instructions that the CPU actually carries out might be
something like this:
1. Load the number from memory location 2001 into the CPU
2. Load the number from memory location 2002 into the CPU
3. Add the two numbers in the CPU
4. Store the result into location 2003
With instructions and numbers represented in binary notations (as
sequences of 0s and 1s)
In a high-level language (eg. Python): c = a + b
Translate a high-level language to a
machine language
• Programs written in a high-level language need to
be translated into the machine language the
computer can execute
• Two ways to do this: a high-level language can be
either compiled or interpreted
Compiling a high-level language
• A compiler is a complex computer program that takes
another program written in a high-level language and
translates it into an equivalent program in the machine
language of some computer
Interpreting a high-level language
• An interpreter is a program that simulates a computer that
understands a high-level language. Rather than translating the source
program into a machine language equivalent, the interpreter analyzes
and executes the source code instruction by instruction as necessary.
• To run a program, both the interpreter and the source are required
each time.
• Interpreted languages tend to have more flexible programming
environment as programs can be developed and run interactively, but
are generally slower than compiled languages.
Python is an interpreted language
• Start the Python interpreter in an interactive mode
• >>> is a Python prompt indicating that the interpreter is waiting for us
to give a command. A complete command is called a statement
Defining a new function in the interactive
mode
 Python allows you put a sequence of statements together to create
a brand-new command called a function.
o The first line tells Python that we are defining a new function
called hello.
o The following lines are indented to show that they are part of the
hello function.
o The blank line lets Python know that the definition is finished
 Notice that the definition did not cause anything to happen. A
function is invoked by typing its name.
Defining a new function with parameters
 Commands can have changeable parts called parameters that are
placed within the parentheses
Now we can called the newly defined function with parameters:
Write Python programs
• Type definitions into a separate file, called module or script. Save the
file on a disk
• Several ways to run the program:
– python chaos.py
– >>> import chaos
# in the interactive mode
• As Python imports the module file, each line executes. It’s just as if
we had typed them one-by-one at the interactive Python prompt.
• Once imported, main() can be re-invoked by typing
>>> import chaos.main()
Inside a Python program
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comments:
o any text from # through the end of a line
o intended for humans, ignored by the Python
defining a function called main
x is variable, used to give a name to a value so that we can refer to later
The statement starting with for is an example of a loop
o A loop is a device that tells Python to do the same thing over and over
again
o The lines indented underneath the loop heading form the body of the
loop
x = 3.9 * x * (1-x) is an assignment statement: the value on the righthand side is computed, and is then stored back (assigned) into the variable on
the left-and side of =.